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- PDB-4jr0: Human procaspase-3 bound to Ac-DEVD-CMK -

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Basic information

Entry
Database: PDB / ID: 4jr0
TitleHuman procaspase-3 bound to Ac-DEVD-CMK
Components
  • Ac-DEVD-CMK
  • Procaspase-3
KeywordsAPOPTOSIS / HYDROLASE/HYDROLASE INHIBITOR / protease / proenzyme / protein-peptide complex / irreversible inhibitor / activity based probe / caspase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cellular response to staurosporine / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / response to anesthetic / Apoptosis induced DNA fragmentation / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / death receptor binding / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / axonal fasciculation / regulation of synaptic vesicle cycle / fibroblast apoptotic process / epithelial cell apoptotic process / Other interleukin signaling / platelet formation / negative regulation of cytokine production / positive regulation of amyloid-beta formation / execution phase of apoptosis / negative regulation of B cell proliferation / Apoptotic cleavage of cellular proteins / pyroptotic inflammatory response / negative regulation of activated T cell proliferation / T cell homeostasis / neurotrophin TRK receptor signaling pathway / B cell homeostasis / negative regulation of cell cycle / response to tumor necrosis factor / cell fate commitment / response to amino acid / response to X-ray / Pyroptosis / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / response to glucose / response to glucocorticoid / response to UV / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / protein maturation / enzyme activator activity / erythrocyte differentiation / hippocampus development / response to nicotine / apoptotic signaling pathway / sensory perception of sound / protein catabolic process / regulation of protein stability / protein processing / response to hydrogen peroxide / response to wounding / neuron differentiation / positive regulation of neuron apoptotic process / response to estradiol / peptidase activity / heart development / protease binding / neuron apoptotic process / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / postsynaptic density / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / glutamatergic synapse / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Rossmann fold - #1460 / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Akz-CMK / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.796 Å
AuthorsThomsen, N.D. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural snapshots reveal distinct mechanisms of procaspase-3 and -7 activation.
Authors: Thomsen, N.D. / Koerber, J.T. / Wells, J.A.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procaspase-3
B: Procaspase-3
C: Ac-DEVD-CMK
D: Ac-DEVD-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7516
Polymers57,6804
Non-polymers712
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-32 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.988, 84.751, 96.641
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Procaspase-3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / ...CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1 / Caspase-3


Mass: 28303.254 Da / Num. of mol.: 2 / Fragment: protease domain (UNP residues 34-277) / Mutation: D175A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Plasmid: Addgene plasmid 29653 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: P42574, caspase-3
#2: Protein/peptide Ac-DEVD-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 536.962 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: Ac-Asp-Glu-Val-Akz-CMK
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10 mM Tris, pH 8.0, 10 mM DTT, 50 mM sodium chloride, 10% PEG3350, 250 mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2011
RadiationMonochromator: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. all: 51104 / Num. obs: 51104 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.059 / Χ2: 1.069 / Net I/σ(I): 18.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.796-1.863.90.6182.250171.13299
1.86-1.943.90.44750071.11299.2
1.94-2.033.90.30150541.09899.6
2.03-2.133.90.21650581.06799.8
2.13-2.2740.14450681.09399.9
2.27-2.4440.10850871.04699.7
2.44-2.6940.08251031.07599.8
2.69-3.0840.05951301.05299.7
3.08-3.883.90.04351800.99199.7
3.88-507.30.03254001.05199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å48.32 Å
Translation2.5 Å48.32 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ELVESrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DKO

2dko


Resolution: 1.796→48.32 Å / Occupancy max: 1 / Occupancy min: 0.15 / SU ML: 0.16 / σ(F): 0 / Phase error: 20.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 2588 5.07 %RANDOM
Rwork0.1627 ---
all0.1643 51040 --
obs0.1643 51020 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.97 Å2 / Biso mean: 21.7796 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 1.796→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 2 423 4164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014051
X-RAY DIFFRACTIONf_angle_d1.2455502
X-RAY DIFFRACTIONf_chiral_restr0.095587
X-RAY DIFFRACTIONf_plane_restr0.005706
X-RAY DIFFRACTIONf_dihedral_angle_d12.6591587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.796-1.83050.2441340.23552599273397
1.8305-1.86790.27291460.22022622276899
1.8679-1.90850.24881300.20922655278599
1.9085-1.95290.22091520.19742664281699
1.9529-2.00170.23051330.190326602793100
2.0017-2.05590.21711500.167926562806100
2.0559-2.11640.21591300.166726792809100
2.1164-2.18470.19041660.162426522818100
2.1847-2.26270.18351520.151126682820100
2.2627-2.35330.21491420.156426842826100
2.3533-2.46040.17881400.159926812821100
2.4604-2.59010.2221470.161726742821100
2.5901-2.75240.20871470.156527282875100
2.7524-2.96490.18031480.16526742822100
2.9649-3.26320.22211240.165927592883100
3.2632-3.73530.19111160.144127532869100
3.7353-4.70540.13671710.13072739291099
4.7054-48.3380.19641600.179128853045100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4844-0.5026-0.02682.34940.68891.780.07990.06720.1202-0.02450.0008-0.2811-0.08060.15010.0170.0732-0.0091-0.01550.09020.00350.127512.37813.404823.797
21.6320.04230.1211.44350.54991.81920.0675-0.04810.03660.0739-0.05080.11750.1164-0.1586-0.00110.0809-0.0083-0.00440.09230.01320.0824-1.7787-2.896222.5654
30.50210.3198-0.24630.5085-0.05881.46250.0694-0.0614-0.00840.1504-0.02030.02010.0316-0.0773-0.00010.126-0.0060.00990.11460.01550.0919-3.38030.07820.6291
42.03050.0869-0.08331.4229-0.22261.84570.09550.12530.2805-0.1073-0.01320.2201-0.1739-0.26080.00430.12760.0488-0.01980.15030.01380.1431-12.20914.104-3.9468
51.92320.7583-0.21331.5089-0.73681.69610.15090.0240.25280.0291-0.01690.0362-0.1522-0.09850.01840.10410.0253-0.00010.10990.00080.0964-4.19811.36851.0694
60.4611-0.3077-0.39340.4262-0.16851.6220.05460.0039-0.022-0.1657-0.0438-0.02890.12280.0758-0.00260.13420.0150.00390.1152-0.01470.0983.7753-2.87290.9984
70.0416-0.0470.02540.0483-0.01480.1220.0251-0.4195-0.16150.35060.08940.2481-0.0058-0.12550.00220.19830.03910.07180.20790.00870.1779-6.16039.048632.3938
80.3316-0.23770.04950.29530.00010.01650.0220.3055-0.1418-0.44480.0892-0.1022-0.01350.0590.01340.2304-0.010.10660.23840.02910.18326.24329.6796-10.6323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 34:187A34 - 187
2X-RAY DIFFRACTION2chain A and resseq 188:247A188 - 247
3X-RAY DIFFRACTION3chain A and resseq 248:277A248 - 277
4X-RAY DIFFRACTION4chain B and resseq 34:143B34 - 143
5X-RAY DIFFRACTION5chain B and resseq 144:228B144 - 228
6X-RAY DIFFRACTION6chain B and resseq 229:277B229 - 277
7X-RAY DIFFRACTION7chain CC1 - 206
8X-RAY DIFFRACTION8chain DD1 - 205

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